Publications

Datta V., Hannenhalli S., Siddharthan R..  2019.  ChIPulate: A comprehensive ChIP-seq simulation pipeline. PLOS Computational Biology. 15:1-32.

Juul JS, Jensen MH, Krishna S.  2019.  Constraints on somite formation in developing embryos.. J R Soc Interface. 16(158):20190451.

Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Das R, Gosavi S.  2019.  A five-residue motif for the design of domain swapping in proteins.. Nat Commun. 10(1):452.

Bhattacharyya A, Gupta A, Kuppusamy L, Mani S, Shukla A, Srivas M, Thattai M.  2019.  A formal methods approach to predicting new features of the eukaryotic vesicle traffic system.

Farheen N, Thattai M.  2019.  Frustration and fidelity in influenza genome assembly.. J R Soc Interface. 16(160):20190411.

Neelamraju S, Wales DJ, Gosavi S.  2019.  Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins.. J Chem Inf Model. 59(5):1703-1708.

Thattai M.  2019.  How contraction has shaped evolution.. Elife. 8

Varahan S, Walvekar A, Sinha V, Krishna S, Laxman S.  2019.  Metabolic constraints drive self-organization of specialized cell groups. Elife. 8:e46735.

Liu G, Patch A, Bahar F, Yllanes D, Welch RD, M Marchetti C, Thutupalli S, Shaevitz JW.  2019.  Self-Driven Phase Transitions Drive Myxococcus xanthus Fruiting Body Formation.. Phys Rev Lett. 122(24):248102.

A. Vishen S, Prost J., Rao M.  2018.  Breakdown of effective temperature, power law interactions and self-propulsion in a momentum conserving active fluid. ArXiv e-prints.

Das SG, Rao M, Iyengar G.  2018.  Cascade of transitions in molecular information theory. Journal of Statistical Mechanics: Theory and Experiment. 2018:093402.

Gupta GD, Dey G, Mg S, Ramalingam B, Shameer K, Thottacherry JJose, Kalappurakkal JMathew, Howes MT, Chandran R, Das A et al..  2018.  Correction: Population Distribution Analyses Reveal a Hierarchy of Molecular Players Underlying Parallel Endocytic Pathways.. PLoS One. 13(9):e0204770.

Datta V, Siddharthan R, Krishna S.  2018.  Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization.. PLoS One. 13(7):e0199771.

Neelamraju S, Gosavi S, Wales DJ.  2018.  Energy Landscape of the Designed Protein Top7.. J Phys Chem B. 122(51):12282-12291.

Thutupalli S, Geyer D, Singh R, Adhikari R, Stone HA.  2018.  Flow-induced phase separation of active particles is controlled by boundary conditions.. Proc Natl Acad Sci U S A. 115(21):5403-5408.

Rao VVHemanth, Gosavi S.  2018.  On the folding of a structurally complex protein to its metastable active state.. Proc Natl Acad Sci U S A. 115(9):1998-2003.

Hossein SRaj, Mandal R, Rao M.  2018.  Interacting passive advective scalars in an active medium. Physical Review E. 98:052608.

Mascarenhas NManuel, Terse VL, Gosavi S.  2018.  Intrinsic Disorder in a Well-Folded Globular Protein. The Journal of Physical Chemistry BThe Journal of Physical Chemistry B. 122(6):1876-1884.

Rupprecht J.-F., A. Vishen S, Shivashankar G.V, Rao M, Prost J..  2018.  Maximal Fluctuations of Confined Actomyosin Gels: Dynamics of the Cell Nucleus. Physical Review LettersPhys. Rev. Lett.. 120(9):098001-.

Thottacherry JJose, Kosmalska AJoanna, Kumar A, Vishen ASingh, Elosegui-Artola A, Pradhan S, Sharma S, Singh PP, Guadamillas MC, Chaudhary N et al..  2018.  Mechanochemical feedback control of dynamin independent endocytosis modulates membrane tension in adherent cells. Nature communications. 9:4217.

Krishna S, Laxman S, Lew DJ.  2018.  A minimal “push–pull” bistability model explains oscillations between quiescent and proliferative cell states. Molecular Biology of the CellMolecular Biology of the Cell. 29(19):2243-2258.

Nandi SKumar, Mandal R, Bhuyan PJyoti, Dasgupta C, Rao M, Gov NS.  2018.  A random first-order transition theory for an active glass. Proceedings of the National Academy of Sciences. 115(30):7688.

Lal A, Krishna S, Seshasayee ASai Narain.  2018.  Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA. G3: Genes, Genomes, Genetics. 8:2079–2089.

Terse VL, Gosavi S.  2018.  The Sensitivity of Computational Protein Folding to Contact Map Perturbations: The Case of Ubiquitin Folding and Function.. J Phys Chem B. 122(49):11497-11507.

Sathe M, Muthukrishnan G, Rae J, Disanza A, Thattai M, Scita G, Parton RG, Mayor S.  2018.  Small GTPases and BAR domain proteins regulate branched actin polymerisation for clathrin and dynamin-independent endocytosis. Nature communications. 9:1835.